A simple method to control over-alignment in the MAFFT multiple sequence alignment program.

ABSTRACT:

Motivation

We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction.

Results

The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, t

SUBMITTER: Katoh K 

PROVIDER: S-EPMC4920119 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature